Memprot GPCR-ModSim

Memprot GPCR-ModSim models and simulates membrane protein systems, including GPCRs, by generating membrane-embedded, solvated, and equilibrated systems ready for molecular dynamics simulations.

Key Features:

• Dual Input Modes: Accepts either a membrane-protein sequence, reporting the associated AlphaFold model, or a 3D structure including quaternary complexes with associated proteins and/or ligands of any kind.
• Membrane Embedding and System Preparation: Produces a membrane-embedded, solvated, and equilibrated system through a molecular dynamics protocol.
• Standalone Modules: Includes PyModSim for 3D modelling and PyMemDyn for membrane embedding and MD equilibration.

Scientific Applications:

• Membrane Protein Modelling: Enables modelling of any membrane protein system beyond class-A G protein-coupled receptors.
• Ligand-Binding Free Energy Calculations: Generates equilibrated systems suitable as starting points for MD simulations including ligand-binding free energy calculations.

Methodology:

The server uses a molecular dynamics protocol for membrane embedding, solvation, and equilibration; standalone modules PyModSim and PyMemDyn handle 3D modelling and membrane embedding with MD equilibration respectively.